大白猪基因组选择在不同应用策略下的比较研究

目前，基因组选择（genomic selection，GS）技术已经在种猪育种中开展，但为获得较高的收益，还需研究一些应用策略，如确定仔猪基因分型个体比例和早期仔猪留种比例。本试验选择温氏集团出生于2011—2016年的大白种猪作为研究对象，共有超过4.5万条的生长测定记录，超过7万条繁殖记录，和2 090个个体的简化基因组测序（GBS）数据，其中，出生于2016年7~12月的440个体作为候选群体。研究性状包括两个生长性状（校正100 kg日龄和校正100 kg背膘厚）和一个繁殖性状（总产仔数）。为对比预测效果，在候选群体进行育种值预测时，按照是否利用其基因型或表型信息分为4种预测方案，比较不同方案的预测可靠性和个体选择指数的排名情况。结果显示，在预测候选群育种值时，利用其表型或基因型信息均比不利用时的预测结果更加可靠。对生长性状终测前、后进行基因组选择指数计算，发现，终测后指数排名前30%的个体都位于终测前指数排名前60%内。若仔猪出生后仅选择常规BLUP预测指数排名前60%的个体，会导致有接近15%的具有优秀潜力的个体被遗漏。本研究建议，对所有新生健康仔猪都进行基因分型并计算基因组选择指数，然后对指数排名靠前60%的个体进行性能测定。

Comparative Analysis of Different Implementation Strategies on Genomic Selection in Large White Pigs

At present, genomic selection (GS) has been applied in pigs breeding, but some implementation strategies, such as the determination of genotyping ratios or early selection rates for piglets, are required to obtain a higher benefit using this technology. The Large White pigs born from 2011 to 2016 at WENS Foodstuff Group Co.，Ltd were chose as the research objects, including more than 45 000 growth measurement records, more than 70 000 reproduction records and 2 090 individuals with genotyping-by-sequencing (GBS) data. The 440 individuals born from July to December in 2016 were used as the candidate individuals. The traits included two growth traits, age at 100 kg and backfat thickness at 100 kg, and one reproduction trait, number of total born. To compare the prediction effects, four prediction scenarios were designed according to including or ignoring the phenotypic or genotypic information of candidate individuals when predicting their breeding values. The predictive reliability of different scenarios and rankings of selection indices of individuals would be compared. The results showed that the results using the phenotypic and genotypic information was more reliable than ignoring them to predict the breeding values of candidate individuals. When genomic selection indices were calculated before and after performances testing for the growth traits, the individuals ranking in the top 30% of indices after testing were all found in the individuals ranking in the top 60% of indices before testing. If the piglets with the top 60% of traditional BLUP indices were only selected, around 15% of individuals with good genetic potentials would be omitted. This study suggests that all healthy piglets after birth are genotyped and their genomic selection indices are calculated, and then the individuals ranking in the top 60% of indices are chose to perform growth measurement.